Comments (9)
All seems to be working.
Now finish the documentation for release.
from mpgap.
Implementation under development in branch issue-15.
from mpgap.
The implementation is already undergoing with something similar to what is done in bacannot samplesheet.
The implementation shall go step-by-step and execution tests must be performed. A workflow will only start to be implemented when the other has been fully developed and tested.
Checklist:
short-reads only
- Implement YAML samplesheet for short-reads only workflows
- execute assembly with paired end reads
- execute assembly with single end reads
- execute assembly with both paired single end reads
long reads only
- Implement YAML samplesheet for long-reads only workflows
- execute assembly with nanopore reads, without nanopolish
- execute assembly with nanopore reads, with nanopolish
- execute assembly with pacbio reads, without gcpp
- execute assembly with pacbio reads, with gcpp
Think about medaka model. It should be defined for each sample in the YAML or it must continue as a "outside-YAML" general parameter that sets the value for all samples?
Hybrid assembly
strategy 1
- Implement YAML samplesheet for hybrid workflows, in strategy 1.
- execute strategy one assembly with paired end reads + nanopore
- execute strategy one assembly with single end reads + nanopore
- execute strategy one assembly with both paired and single end reads + nanopore
- execute strategy one assembly with paired end reads + pacbio
- execute strategy one assembly with single end reads + pacbio
- execute strategy one assembly with both paired and single end reads + pacbio
strategy 2
- Implement YAML samplesheet for hybrid workflows, in strategy 2.
- execute strategy two assembly with paired end reads + nanopore
- execute strategy two assembly with single end reads + nanopore
- execute strategy two assembly with both paired and single end reads + nanopore
- execute strategy two assembly with paired end reads + pacbio
- execute strategy two assembly with single end reads + pacbio
- execute strategy two assembly with both paired and single end reads + pacbio
from mpgap.
Almost finished!
It was required to make some changes in the way the channels were called and created. So now everything seems properly implemented ...
However, I will have to execute all the tests again to make sure everything is ok and it can be released.
While the tests run, I will start working on the new documentation.
from mpgap.
Little update on tests:
- The use of gcpp in the samplesheet did not work. Check how it is differing from the single sample workflow and try to create the input tuple similar to it, since it is working.
from mpgap.
Found an issue on how nanopolish was being called! It is now solved, with proper multi-thread and the corrected module will be available in v2.4, together with this multi-sample workflow release.
from mpgap.
Working on documentation for release!
from mpgap.
This implementation is provoking major changes in the pipeline, therefore, it will delay a littler bit more since we are trying to decide the best implementation for the parameters in and outside the YAML samplesheet in order to be the less confusing possible.
When finished, it will trigger a major release version, v3.0
from mpgap.
This implementation has now been made available.
from mpgap.
Related Issues (20)
- add trycycler
- add 3 hybrid strategy HOT 1
- Requesting support with error "Explicit 'name separator' in class" HOT 4
- update tool versions
- add homopolish tool HOT 1
- Add skip parameter for sreads polishers and fix multiqc report names HOT 1
- Incomplete pipeline and different errors when using nanopore reads files with different sizes (900 mb vs 11Gb) HOT 18
- Add hifiasm for long reads assemble HOT 5
- 100% missing in Busco HOT 4
- Enhance documentation (paper review) HOT 2
- Add example of non-bacterial dataset analysis (paper review) HOT 1
- problem with longreads_only assembly HOT 4
- Add a simple parameter to handle starting memory settings HOT 1
- add automatic samplesheet for bacannot
- add the possibility of running directly from SRA IDs
- When not giving `--genome_size` for long reads, message goes to log and not console HOT 1
- allow hifiasm to use hi-c and parental data
- should hifiasm be executed only when user says reads are high quality? HOT 1
- Enhance polishing and downstream as hybracter
- error in running MpGAP with SRR8482585_30X_{1,2}.fastq.gz and SRX5299443_30X.fastq.gz HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from mpgap.